I did not like the first Prototype. Radical's open-world action title put you into the mutated skin of a super-cannibal that ate people in his quest for vengeance. Playing as aggrieved scientist Alex Mercer made me feel creepy, as I generally am not interested in eating people. The story and the reasons it gave for eating other humans didn't make much sense.
Turns out that Radical glommed on to those facts. In an interview at Gamasutra, design director Matt Armstrong talks about the Activision dev team's re-evaluation of the first Prototype:
"It was clear from the outset we needed to tell a story more people could understand, ideally with a protagonist that was more relatable as well, with a motivation clearly understandable to the player," he added. From Prototype 1, the team learned it had to present mission challenges in better context. "There was a massive missed opportunity to take the world that we've built and start to give it a lot more in the way of personality."
I was surprised when Prototype 2 was announced, given the stumbles of the first game. More than any pre-order ability or urban hunting mechanics, the statements above get me excited for Prototype 2. The idea that Radical will get a second chance to improve the Prototype universe is a rare chance and, from the interview with Armstrong, it seems like they're trying to make the most of it.